Step by step guide

Introduction

FungiExpresZ is a web based platform to analyze and visualize fungal gene expression data. It allows you to analyze and visualize …

1. NCBI SRA fungal gene expression data.
2. User uploaded gene expression data.
3. NCBI SRA data combined with User uploaded data (1+2).

It contains normalized gene expression values of more than 12,000 NCBI SRA data from 8 different fungal species and, gene annotations and GO data of more than 100 different fungal species. For 3 strategies mentioned above, you can generate 12 different data exploratory plots and 6 different GO plots.

Data exploratory plots

1. Scatter plot
2. Multi-scatter plot
3. CorrHeatBox
4. Density plot
5. Histogram
6. Joy plot
7. Box plot
8. Violin plot
9. Bar plot
10. PCA plot
11. Line plot
12. Heatmap

GO plots

1. EMAP plot
2. CNET plot
3. Dot plot
4. Bar plot
5. Heat box
6. Upset plot

The purpose of this document is to explain all the key functionalities and methods used in this website wherever necessary.

User manual

Source

There are three ways in which you can access FungiExpresZ.

1. Online

FungiExpresZ has been hoisted on shinyapps.io and can be accessed through the link https://cparsania.shinyapps.io/FungiExpresZ/. This is one of the quickest way to access the FungiExpresZ. However, due to limited computational resources, I would recommend this approach only when the size of the data is comparatively small (< 10 MB) and/or you are in a need of quick figure out of your data. Current setup allows approx. 30 users to concurrently

2. As an R package

3. As a docker container

Home screen

FIGURE 1: FungiExpresZ home screen

Select/Upload data

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Select SRA data

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FIGURE 2: FungiExpresZ select SRA data

Upload user data

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FIGURE 3: FungiExpresZ upload user data

Assign groups

Sample groups

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FIGURE 4: FungiExpresZ define sample groups

Gene groups

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FIGURE 5: FungiExpresZ define gene groups

View active groups

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Plot panels

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Plot input panels

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Scatter plot

FIGURE XXX: FungiExpresZ Scatter plot input panel

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Multi-scatter plot, CorrHeatBox, Density plot, Histogram, Joy plot, Box plot, Violin plot and PCA plot

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FIGURE XXX: FungiExpresZ Multi-scatter plot, CorrHeatBox, Density plot, Histogram, Joy plot, Box plot. Violin plot and PCA plot input panel

Bar plot inputs

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FIGURE XXX:FungiExpresZ Bar plot input panel

Line plot inputs

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FIGURE XXX: FungiExpresZ Line plot input panel

Heatmap inputs

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FIGURE XXX: FungiExpresZ Heatmap inputs

Plot settings

// TO DO ### Common plot settings

FIGURE XXX: FungiExpresZ common plot settings : Theme and Legend (left), Labels & Title (right)

Plot specific settings

Scatter plot

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FIGURE XXX: FungiExpresZ Scatter plot advance options

Multi-scatter plot

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FIGURE XXX: FungiExpresZ Multi-scatter plot advance options

CorrHeatBox

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FIGURE XXX: FungiExpresZ Corr heat-box advance options

Density plot

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FIGURE XXX: FungiExpresZ Density plot advance options

Histogram

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FIGURE XXX: FungiExpresZ Histogram advance options

Joy plot

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FIGURE XXX: FungiExpresZ Joy plot advance options

Box plot

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FIGURE XXX: FungiExpresZ Box plot advance options

Violin plot

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FIGURE XXX: FungiExpresZ Violin plot advance options

Bar plot

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FIGURE XXX: FungiExpresZ Bar plot advance options

PCA plot

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FIGURE XXX: FungiExpresZ PCA plot advance options

Line plot

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FIGURE XXX: FungiExpresZ Line plot advance options

Heatmap

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GO analysis and visualizations

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FIGURE XXX: FungiExpresZ GO analysis inputs

GO plots specific settings

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Dot plot and Bar plot

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FIGURE XXX: FungiExpresZ GO Dot plot and Bar plot advance options

EMAP plot

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FIGURE XXX: FungiExpresZ GO EMAP plot advance options

CNET plot

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FIGURE XXX: FungiExpresZ GO CNET plot advance options

UPSET plot

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FIGURE XXX: FungiExpresZ GO Upset plot advance options

Heat plot

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FIGURE XXX: FungiExpresZ GO Heat plot advance options

Other panels

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About

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FIGURE XXX: FungiExpresZ Overview page

FIGURE XXX: FungiExpresZ Tutorial page

Downloads

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FIGURE XXX: FungiExpresZ Downloads --> Gene expression data page

FIGURE XXX: FungiExpresZ Download --> GO data page

News & Updates

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FIGURE XXX: FungiExpresZ News & Updates page

Citations

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FIGURE XXX: FungiExpresZ Citations page